[SciPy-dev] scipy 0.6.0 tests kill python interpreter

Sat Dec 1 16:54:37 EST 2007

On Dec 1, 2007 10:44 PM, Robert Kern <robert.kern at gmail.com> wrote:
>
> Ondrej Certik wrote:
> > Hi,
> >
> > if I install scipy 0.6.0 on Debian and run tests, it kills the
> > interpreter with Illegal instruction.
> >
> > More details here:
> >
> > http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=452991
> >
> > Is anyone able to reproduce it on their system, or is it just related
> > to Debian? Could you please send me
> > the correct run of tests, so that I can discover where exactly it differs?
>
> Try scipy.test(verbosity=1). This will print the name of the test before it runs
> the test. Also, try running Python under gdb so we can get a backtrace.

It doesn't seem to help much:

>>> import scipy
s>>> scipy.test(verbosity=1)
  Found 9 tests for scipy.cluster.vq
  Found 18 tests for scipy.fftpack.basic
  Found 4 tests for scipy.fftpack.helper
  Found 20 tests for scipy.fftpack.pseudo_diffs
  Found 1 tests for scipy.integrate
  Found 10 tests for scipy.integrate.quadpack
  Found 3 tests for scipy.integrate.quadrature
  Found 6 tests for scipy.interpolate
  Found 6 tests for scipy.interpolate.fitpack
  Found 4 tests for scipy.io.array_import
  Found 28 tests for scipy.io.mio
  Found 13 tests for scipy.io.mmio
  Found 5 tests for scipy.io.npfile
  Found 4 tests for scipy.io.recaster
  Found 16 tests for scipy.lib.blas
  Found 128 tests for scipy.lib.blas.fblas

****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
  then scipy uses flapack instead of clapack.
****************************************************************

  Found 42 tests for scipy.lib.lapack
  Found 41 tests for scipy.linalg.basic
<module 'scipy.linalg.fblas' from
'/usr/lib/python2.4/site-packages/scipy/linalg/fblas.so'>
  Found 16 tests for scipy.linalg.blas
  Found 72 tests for scipy.linalg.decomp
  Found 128 tests for scipy.linalg.fblas
  Found 6 tests for scipy.linalg.iterative
  Found 4 tests for scipy.linalg.lapack
  Found 7 tests for scipy.linalg.matfuncs
  Found 9 tests for scipy.linsolve.umfpack
  Found 2 tests for scipy.maxentropy
  Found 3 tests for scipy.misc.pilutil
  Found 399 tests for scipy.ndimage
  Found 5 tests for scipy.odr
  Found 8 tests for scipy.optimize
  Found 1 tests for scipy.optimize.cobyla
  Found 10 tests for scipy.optimize.nonlin
  Found 4 tests for scipy.optimize.zeros
  Found 5 tests for scipy.signal.signaltools
  Found 4 tests for scipy.signal.wavelets
  Found 152 tests for scipy.sparse
  Found 342 tests for scipy.special.basic
  Found 3 tests for scipy.special.spfun_stats
  Found 107 tests for scipy.stats
  Found 73 tests for scipy.stats.distributions
  Found 10 tests for scipy.stats.morestats
  Found 0 tests for __main__
.../usr/lib/python2.4/site-packages/scipy/cluster/vq.py:477:
UserWarning: One of the clusters is empty. Re-run kmean with a
different initialization.
  warnings.warn("One of the clusters is empty. "
exception raised as expected: One of the clusters is empty. Re-run
kmean with a different initialization.
................................................Residual: 1.05006950608e-07
..................../usr/lib/python2.4/site-packages/scipy/interpolate/fitpack2.py:458:
UserWarning:
The coefficients of the spline returned have been computed as the
minimal norm least-squares solution of a (numerically) rank deficient
system (deficiency=7). If deficiency is large, the results may be
inaccurate. Deficiency may strongly depend on the value of eps.
  warnings.warn(message)
......
Don't worry about a warning regarding the number of bytes read.
Warning: 1000000 bytes requested, 20 bytes read.
.........................................................................caxpy:n=4
..caxpy:n=3
....ccopy:n=4
..ccopy:n=3
.............cscal:n=4
....cswap:n=4
..cswap:n=3
.....daxpy:n=4
..daxpy:n=3
....dcopy:n=4
..dcopy:n=3
.............dscal:n=4
....dswap:n=4
..dswap:n=3
.....saxpy:n=4
..saxpy:n=3
....scopy:n=4
..scopy:n=3
.............sscal:n=4
....sswap:n=4
..sswap:n=3
.....zaxpy:n=4
..zaxpy:n=3
....zcopy:n=4
..zcopy:n=3
.............zscal:n=4
....zswap:n=4
..zswap:n=3
.....................................................................................
****************************************************************
WARNING: cblas module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
  then scipy uses fblas instead of cblas.
****************************************************************

...........................................................................................caxpy:n=4
..caxpy:n=3
....ccopy:n=4
..ccopy:n=3
.............cscal:n=4
....cswap:n=4
..cswap:n=3
.....daxpy:n=4
..daxpy:n=3
....dcopy:n=4
..dcopy:n=3
.............dscal:n=4
....dswap:n=4
..dswap:n=3
.....saxpy:n=4
..saxpy:n=3
....scopy:n=4
..scopy:n=3
.............sscal:n=4
....sswap:n=4
..sswap:n=3
.....zaxpy:n=4
..zaxpy:n=3
....zcopy:n=4
..zcopy:n=3
.............zscal:n=4
....zswap:n=4
..zswap:n=3
..........
****************************************************************
WARNING: clapack module is empty
-----------
See scipy/INSTALL.txt for troubleshooting.
Notes:
* If atlas library is not found by numpy/distutils/system_info.py,
  then scipy uses flapack instead of clapack.
****************************************************************

...Result may be inaccurate, approximate err = 2.90112626413e-09
...Result may be inaccurate, approximate err = 7.27595761418e-12
......Use minimum degree ordering on A'+A.
..Use minimum degree ordering on A'+A.
...Use minimum degree ordering on A'+A.
............................................................................................................./usr/lib/python2.4/site-packages/scipy/ndimage/interpolation.py:41:
UserWarning: Mode "reflect" may yield incorrect results on boundaries.
Please use "mirror" instead.
  warnings.warn('Mode "reflect" may yield incorrect results on '
.............................................................................................Illegal
instruction

But when running through gdb, it says:

  warnings.warn('Mode "reflect" may yield incorrect results on '
.............................................................................................
Program received signal SIGILL, Illegal instruction.
[Switching to Thread 0xb7e278c0 (LWP 28932)]
0xb6b83d43 in ?? ()
   from /usr/lib/python2.4/site-packages/scipy/ndimage/_nd_image.so
(gdb) bt
#0  0xb6b83d43 in ?? ()
   from /usr/lib/python2.4/site-packages/scipy/ndimage/_nd_image.so
#1  0xbf99bdd8 in ?? ()
#2  0xb6b87211 in NI_GenericFilter ()
   from /usr/lib/python2.4/site-packages/scipy/ndimage/_nd_image.so
Backtrace stopped: frame did not save the PC
(gdb)

I don't have time to dig into this and fix it myself, but if you tell
me what else to try, I will.

Thanks a lot,
Ondrej